In China, reindeer, a valuable wildlife resource, only exists in the Genhe area of Inner Mongolia. Despite their economic benefits, reindeer are listed as critically endangered in China mainly owing to loss and degradation of habitat. To sustainably conserve the reindeer population and their habitat, it is necessary to study the habitat utilization of reindeer. In September and October 2012 and 2013, autumn habitat selection and utilization patterns of reindeer were studied using both line and strip-transect surveys. Twenty-five ecological variables were measured and compared for 234 sites in the Genhe area of northwestern China. Seventy-two of all the sampling sites were designated as used habitat plots, and the others as control, non-used plots. Principal component analysis (PCA) was used to extract the key factors influencing habitat selection. The results indicated that, compared to the non-used habitat plots, reindeer selected autumn habitats with comparatively high altitude (948.68±1.10 m), arbor canopy (12.60±1.99%), arbor density (6.92±0.75/400 m2), arbor diameter body height (DBH) (24.46±1.77 cm), arbor height (6.33±0.47 m), shrub cover (42.14±2.22%), muscus-lichen cover (11.94±0.98%) and more stump (4.61±0.44/400 m) and fallen-wood (2.08±0.25/400 m2), but with comparatively low ground-plant cover (83.58±1.03%), snow depth (no snow), snow cover (no snow) and withered-grass cover (2.08±0.25%). Moreover, the reindeer also selected habitats with intermediate upper slope positions (70.8%) in south and west slopes which were located mainly in conifer forest (56.9%) and with poor lee condition (52.8%), relative proximity to water sources (< 1 000 m, 68.1%), but certain distance from anthropogenic disturbance (≥ 500 m, 51.4%) and indigenous residence (≥ 500 m, 51.4%). The PCA results showed that the “Disturbance factor” (i.e. distance from residence and other human influence, altitude, slope position etc. ), “Tree factor” (i.e. vegetation type, arbor DBH, arbor height, and arbor density etc.), “Habitat-ground factor” (i.e. shrub cover, stump, fallen-wood and ground-plant cover), “Concealment factor”(i.e. concealment) and “Slope aspect factor” (i.e. Slope aspect) were the most important factors influencing the habitat selection of reindeer in autumn. In summary, the results indicated the autumn habitat selection of reindeer is a multidimensional process, through which reindeer adapts to the ecological needs, in particular food accessibility and avoidance of disturbance from local indigenous communities.